Structure-guided engineering of an aptamer–PROTAC for targeted degradation of vaccinia-related kinase 1

Abstract

Vaccinia-related kinase 1 (VRK1) is an oncogenic serine/threonine kinase implicated in tumor progression, yet it remains an intractable target for catalytic degradation. Herein, we report the structure-guided design of a first aptamer–PROTAC chimera for potent and selective degradation of VRK1. Through structure-guided computational truncation and optimization of a parent DNA aptamer, we engineered a high-affinity variant (T4) with a 2.4-fold improved binding affinity (KD = 0.61 nM) and enhanced selectivity over the homologous kinase VRK2. Conjugating T4 to a CRBN E3 ligase ligand via a flexible linker produced PROTAC-e, which induced rapid, sustained, and dose-dependent VRK1 degradation in HeLa cells, with a DC50 of 105.8 nM and Dmax of 91%. Degradation was mechanistically confirmed to depend on the ubiquitin-proteasome system. Functionally, PROTAC-e elicited potent anti-proliferative activity (IC50 = 193.8 nM) and S-phase arrest, directly linking VRK1 depletion to antitumor efficacy. This work not only provides a first aptamer–PROTAC targeting VRK1, a previously intractable kinase, but also establishes a generalizable strategy for the rational design of aptamer–PROTACs, opening a route to target kinases beyond conventional small-molecule scaffolds.